Do you know what you use to modprobe for lirc? This mysteriously happens to me when I reboot on FC 5 on my MythTV box (can't figure out why, but I'm looking into it), but I can:
service lirc start
...and all is well!
Check to see what module you actually load for lirc. I know if you are using the Hauppauge PVR-type remotes (on the offhand chance), you modprobe what is above.